{"doi":"10.1101/2022.06.28.22276835","title":"Seq-ing the SINEs of Central Nervous System Tumors in Cerebrospinal Fluid DNA","abstract":"Abstract Lesions within the brain cavity pose critical challenges for diagnostics, particularly distinction between cancerous and non-cancerous lesions. We here introduce an analytic technique called Real-CSF to detect cancers of the central nervous system from evaluation of DNA in the cerebrospinal fluid (CSF). Short interspersed nuclear elements (SINEs) from throughout the genome are PCR-amplified with a single primer pair and the PCR products are evaluated by next generation sequencing. Real-CSF uses machine learning to assess three features from the sequencing data – gains or losses of 39 chromosome arms, focal amplifications, and somatic nucleotide variants. Real-CSF was applied to 282 CSF samples and correctly classified 71 % of 187 cancers and misclassified only 4.2% of 95 non-neoplastic lesions in the brain.","journal":"medRxiv","year":2022,"id":309539,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":0,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9575,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2022-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":1004828,"name":"Samuel M. Curtis","orcid":null,"position":1,"is_corresponding":false},{"id":990774,"name":"Mahmoud Summers","orcid":"0000-0003-2258-6076","position":2,"is_corresponding":false},{"id":30071,"name":"Tej D. Azad","orcid":"0000-0001-7823-4294","position":3,"is_corresponding":false},{"id":334511,"name":"Jordina Rincón-Torroella","orcid":"0000-0003-4798-8231","position":4,"is_corresponding":false},{"id":783688,"name":"Bracha Erlanger Avigdor","orcid":"0000-0002-5031-8303","position":5,"is_corresponding":false},{"id":456343,"name":"Jonathan A. Dudley","orcid":"0000-0002-5189-9568","position":6,"is_corresponding":false},{"id":483440,"name":"Joshua Materi","orcid":"0000-0001-9786-9068","position":7,"is_corresponding":false},{"id":927981,"name":"Divyaansh Raj","orcid":"0000-0002-7249-0200","position":8,"is_corresponding":false},{"id":1004513,"name":"Sumil K. Nair","orcid":"0000-0002-9937-7478","position":9,"is_corresponding":false},{"id":969327,"name":"Debarati Bhanja","orcid":"0000-0002-0591-5547","position":10,"is_corresponding":false},{"id":1004829,"name":"Kyle Touhy","orcid":null,"position":11,"is_corresponding":false},{"id":275559,"name":"Lisa Dobbyn","orcid":"0000-0002-3159-189X","position":12,"is_corresponding":false},{"id":275560,"name":"Maria Popoli","orcid":"0000-0003-2151-7749","position":13,"is_corresponding":false},{"id":2237,"name":"Janine Ptak","orcid":"0000-0003-1934-8739","position":14,"is_corresponding":false},{"id":1004830,"name":"Nadine T. Nehme","orcid":null,"position":15,"is_corresponding":false},{"id":2238,"name":"Natalie Silliman","orcid":"0000-0002-5198-9037","position":16,"is_corresponding":false},{"id":432151,"name":"Cheríe Blair","orcid":"0000-0001-6535-0018","position":17,"is_corresponding":false},{"id":822135,"name":"Kathy Judge","orcid":null,"position":18,"is_corresponding":false},{"id":459882,"name":"Gary L. Gallia","orcid":"0000-0001-6438-7329","position":19,"is_corresponding":false},{"id":1004514,"name":"Mari L. Groves","orcid":"0000-0002-4938-897X","position":20,"is_corresponding":false},{"id":664765,"name":"Christopher M. Jackson","orcid":"0000-0002-5958-2004","position":21,"is_corresponding":false},{"id":481521,"name":"Eric M. Jackson","orcid":"0000-0001-9306-9290","position":22,"is_corresponding":false},{"id":347407,"name":"John Laterra","orcid":"0000-0002-2983-5365","position":23,"is_corresponding":false},{"id":242992,"name":"Michael Lim","orcid":"0000-0003-0523-3076","position":24,"is_corresponding":false},{"id":284949,"name":"Debraj Mukherjee","orcid":"0000-0002-5403-8237","position":25,"is_corresponding":false},{"id":383826,"name":"Jon Weingart","orcid":"0009-0008-8931-7456","position":26,"is_corresponding":false},{"id":254631,"name":"Jarushka Naidoo","orcid":"0000-0002-3470-8686","position":27,"is_corresponding":false},{"id":32692,"name":"Carl J. Koschmann","orcid":"0000-0002-0825-7615","position":28,"is_corresponding":false},{"id":1004831,"name":"Natalya Smith","orcid":null,"position":29,"is_corresponding":false},{"id":463567,"name":"Karisa C. Schreck","orcid":"0000-0001-7181-3269","position":30,"is_corresponding":false},{"id":250734,"name":"Carlos A. Pardo","orcid":"0000-0002-4128-5335","position":31,"is_corresponding":false},{"id":228899,"name":"Michael Glantz","orcid":"0000-0003-4877-5094","position":32,"is_corresponding":false},{"id":62902,"name":"Matthias Holdhoff","orcid":"0000-0002-3285-3484","position":33,"is_corresponding":false},{"id":2256,"name":"Kenneth W. Kinzler","orcid":"0000-0001-5591-1176","position":34,"is_corresponding":false},{"id":2254,"name":"Nickolas Papadopoulos","orcid":"0000-0001-7135-7451","position":35,"is_corresponding":false},{"id":2255,"name":"Bert Vogelstein","orcid":"0000-0003-0766-3854","position":36,"is_corresponding":false},{"id":24634,"name":"Chetan Bettegowda","orcid":"0000-0001-9991-7123","position":37,"is_corresponding":false},{"id":109480,"name":"Christopher Douville","orcid":"0000-0002-2510-4151","position":0,"is_corresponding":true}],"reference_count":34,"raw_metadata":{"citation_network_status":"fetched"},"created_at":"2026-07-19T00:33:11.579763Z","pmid":null,"pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}